Prepare the Data
Create a Data Frame
- Create a data frame with publications as rows and properties as columns.
data <-
matrix(
data = unlist( data.loaded ),
ncol = 4,
byrow = TRUE
)
colnames( data ) <-
c(
"Status",
"Title",
"Info",
"Type"
)
data <-
data.frame(
data,
stringsAsFactors = FALSE
)
head( data )
## Status
## 1 Published
## 2 Published
## 3 Published
## 4 Published
## 5 Published
## 6 Published
## Title
## 1 Associations of hypoglycemia, glycemic variability and risk of cardiac arrhythmias in insulin-treated patients with type 2 diabetes: a prospective, observational study
## 2 The effectiveness of e-learning in patient education delivered to patients with rheumatoid arthritis: The WebRA study-protocol for a pragmatic randomised controlled trial
## 3 The Association Between Cardiovascular Autonomic Function and Changes in Kidney and Myocardial Function in Type 2 Diabetes and Healthy Controls
## 4 Cardiovascular Events with Finerenone in Kidney Disease and Type 2 Diabetes
## 5 Translation and validation of the Canadian assessment of physical literacy-2 in a Danish sample
## 6 Medical therapies for prevention of cardiovascular and renal events in patients with atrial fibrillation and diabetes mellitus
## Info
## 1 Andersen, A., Bagger, J. I., Sørensen, S. K., Baldassarre, M. P. A., Pedersen-Bjergaard, U., Forman, J. L., Gislason, G., Lindhardt, T. B., Knop, F. K. & Vilsbøll, T., 24 Dec 2021, In: Cardiovascular Diabetology. 20, 1, p. 241 241.
## 2 Raunsbæk Knudsen, L., Lomborg, K., Ndosi, M., Hauge, E-M. & de Thurah, A., 20 Dec 2021, In: BMC Rheumatology. 5, 1, p. 57 57.
## 3 Laursen, J. C., Rasmussen, I. K. B., Zobel, E. H., Hasbak, P., von Scholten, B. J., Holmvang, L., Ripa, R. S., Hansen, C. S., Frimodt-Moeller, M., Kjaer, A., Rossing, P. & Hansen, T. W., 13 Dec 2021, In: Frontiers in Endocrinology. 12, p. 780679 780679.
## 4 Pitt, B., Filippatos, G., Agarwal, R., Anker, S. D., Bakris, G. L., Rossing, P., Joseph, A., Kolkhof, P., Nowack, C., Schloemer, P., Ruilope, L. M., FIGARO-DKD Investigators & Pedersen-Bjergaard, U., 9 Dec 2021, In: The New England journal of medicine. 385, 24, p. 2252-2263 12 p.
## 5 Elsborg, P., Melby, P. S., Kurtzhals, M., Tremblay, M. S., Nielsen, G. & Bentsen, P., 9 Dec 2021, In: BMC PUBLIC HEALTH. 21, 1, p. 2236 2236.
## 6 Fauchier, L., Boriani, G., de Groot, J. R., Kreutz, R., Rossing, P. & Camm, A. J., 7 Dec 2021, In: Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology. 23, 12, p. 1873-1891 19 p.
## Type
## 1 Research output: Contribution to journal › Journal article › Research › peer-review
## 2 Research output: Contribution to journal › Journal article › Research › peer-review
## 3 Research output: Contribution to journal › Journal article › Research › peer-review
## 4 Research output: Contribution to journal › Journal article › Research › peer-review
## 5 Research output: Contribution to journal › Journal article › Research › peer-review
## 6 Research output: Contribution to journal › Journal article › Research › peer-review
Subset by Publication Type
- Include journal articles and review articles in the analysis.
table( data$"Type" )
##
## Research output: Contribution to journal › Comment/debate › Research › peer-review
## 13
## Research output: Contribution to journal › Conference abstract in journal › Research › peer-review
## 6
## Research output: Contribution to journal › Editorial › Research › peer-review
## 3
## Research output: Contribution to journal › Journal article › Research › peer-review
## 278
## Research output: Contribution to journal › Letter › Research › peer-review
## 7
## Research output: Contribution to journal › Review › Research › peer-review
## 32
is.included <-
grepl(
x = data$"Type",
pattern = "(Journal article)|(Review)"
)
data <- data[ is.included, ]
Create Additional Properties
- Separate authors from the information column, which also contains the publication date and the journal reference.
# Split by the date text.
tmp <-
stringr::str_split_fixed(
string = data[ , 3 ],
pattern = "(\\,\\s([0-9]+\\s)?([A-Z][a-z][a-z]\\s)?2021\\,\\s)",
n = 2
)
colnames( tmp ) <-
c(
"Authors",
"Reference"
)
tmp <-
data.frame(
tmp,
stringsAsFactors = FALSE
)
data <-
dplyr::bind_cols(
data,
tmp
)
str( data )
## 'data.frame': 310 obs. of 6 variables:
## $ Status : chr "Published" "Published" "Published" "Published" ...
## $ Title : chr "Associations of hypoglycemia, glycemic variability and risk of cardiac arrhythmias in insulin-treated patients "| __truncated__ "The effectiveness of e-learning in patient education delivered to patients with rheumatoid arthritis: The WebRA"| __truncated__ "The Association Between Cardiovascular Autonomic Function and Changes in Kidney and Myocardial Function in Type"| __truncated__ "Cardiovascular Events with Finerenone in Kidney Disease and Type 2 Diabetes" ...
## $ Info : chr "Andersen, A., Bagger, J. I., Sørensen, S. K., Baldassarre, M. P. A., Pedersen-Bjergaard, U., Forman, J. L., Gis"| __truncated__ "Raunsbæk Knudsen, L., Lomborg, K., Ndosi, M., Hauge, E-M. & de Thurah, A., 20 Dec 2021, In: BMC Rheumatology. 5, 1, p. 57 57." "Laursen, J. C., Rasmussen, I. K. B., Zobel, E. H., Hasbak, P., von Scholten, B. J., Holmvang, L., Ripa, R. S., "| __truncated__ "Pitt, B., Filippatos, G., Agarwal, R., Anker, S. D., Bakris, G. L., Rossing, P., Joseph, A., Kolkhof, P., Nowac"| __truncated__ ...
## $ Type : chr "Research output: Contribution to journal › Journal article › Research › peer-review" "Research output: Contribution to journal › Journal article › Research › peer-review" "Research output: Contribution to journal › Journal article › Research › peer-review" "Research output: Contribution to journal › Journal article › Research › peer-review" ...
## $ Authors : chr "Andersen, A., Bagger, J. I., Sørensen, S. K., Baldassarre, M. P. A., Pedersen-Bjergaard, U., Forman, J. L., Gis"| __truncated__ "Raunsbæk Knudsen, L., Lomborg, K., Ndosi, M., Hauge, E-M. & de Thurah, A." "Laursen, J. C., Rasmussen, I. K. B., Zobel, E. H., Hasbak, P., von Scholten, B. J., Holmvang, L., Ripa, R. S., "| __truncated__ "Pitt, B., Filippatos, G., Agarwal, R., Anker, S. D., Bakris, G. L., Rossing, P., Joseph, A., Kolkhof, P., Nowac"| __truncated__ ...
## $ Reference: chr "In: Cardiovascular Diabetology. 20, 1, p. 241 241." "In: BMC Rheumatology. 5, 1, p. 57 57." "In: Frontiers in Endocrinology. 12, p. 780679 780679." "In: The New England journal of medicine. 385, 24, p. 2252-2263 12 p." ...
Split Individual Authors
- Separate individual authors, who are joined by comma or &-sign.
- This creates a list, where each item corresponds to a publication, and the contents of the item is a character vector containing the names of the authors in the respective publication.
authors <-
stringr::str_split(
string = data$"Authors",
pattern = "(\\.\\, )|(\\. \\& )"
)
head( authors )
## [[1]]
## [1] "Andersen, A" "Bagger, J. I" "Sørensen, S. K"
## [4] "Baldassarre, M. P. A" "Pedersen-Bjergaard, U" "Forman, J. L"
## [7] "Gislason, G" "Lindhardt, T. B" "Knop, F. K"
## [10] "Vilsbøll, T."
##
## [[2]]
## [1] "Raunsbæk Knudsen, L" "Lomborg, K" "Ndosi, M"
## [4] "Hauge, E-M" "de Thurah, A."
##
## [[3]]
## [1] "Laursen, J. C" "Rasmussen, I. K. B" "Zobel, E. H"
## [4] "Hasbak, P" "von Scholten, B. J" "Holmvang, L"
## [7] "Ripa, R. S" "Hansen, C. S" "Frimodt-Moeller, M"
## [10] "Kjaer, A" "Rossing, P" "Hansen, T. W."
##
## [[4]]
## [1] "Pitt, B"
## [2] "Filippatos, G"
## [3] "Agarwal, R"
## [4] "Anker, S. D"
## [5] "Bakris, G. L"
## [6] "Rossing, P"
## [7] "Joseph, A"
## [8] "Kolkhof, P"
## [9] "Nowack, C"
## [10] "Schloemer, P"
## [11] "Ruilope, L. M"
## [12] "FIGARO-DKD Investigators & Pedersen-Bjergaard, U."
##
## [[5]]
## [1] "Elsborg, P" "Melby, P. S" "Kurtzhals, M" "Tremblay, M. S"
## [5] "Nielsen, G" "Bentsen, P."
##
## [[6]]
## [1] "Fauchier, L" "Boriani, G" "de Groot, J. R" "Kreutz, R"
## [5] "Rossing, P" "Camm, A. J."
Network of Authors
Initialize the Adjacency Matrix
- Authors-by-authors Adjacency matrix
adjacency.mat <-
array(
data = 0,
dim = c( 1, 1 ) * length( authors.unique )
)
rownames( adjacency.mat ) <-
colnames( adjacency.mat ) <-
authors.unique
str( adjacency.mat )
## num [1:2038, 1:2038] 0 0 0 0 0 0 0 0 0 0 ...
## - attr(*, "dimnames")=List of 2
## ..$ : chr [1:2038] "'t Hart LM" "Aaby P" "Aadahl M" "Aagaard-Hansen J" ...
## ..$ : chr [1:2038] "'t Hart LM" "Aaby P" "Aadahl M" "Aagaard-Hansen J" ...
str(
object = adjacency.mat,
vec.len = 5
)
## num [1:2038, 1:2038] 0 0 0 0 0 0 0 0 0 0 0 0 ...
## - attr(*, "dimnames")=List of 2
## ..$ : chr [1:2038] "'t Hart LM" "Aaby P" "Aadahl M" "Aagaard-Hansen J" "Aalborg GL" ...
## ..$ : chr [1:2038] "'t Hart LM" "Aaby P" "Aadahl M" "Aagaard-Hansen J" "Aalborg GL" ...
Compute the Co-Occurrence of Author Pairs
- Go through all publications ‘i’.
- Add up the co-occurrence count for the authors in the publication ‘i’.
for ( i in 1:length( authors ) ) {
tmp <- rownames( adjacency.mat ) %in% authors[[ i ]]
adjacency.mat[ tmp, tmp ] <- adjacency.mat[ tmp, tmp ] + 1
}
str( adjacency.mat )
## num [1:2038, 1:2038] 2 0 0 0 0 0 0 0 0 0 ...
## - attr(*, "dimnames")=List of 2
## ..$ : chr [1:2038] "'t Hart LM" "Aaby P" "Aadahl M" "Aagaard-Hansen J" ...
## ..$ : chr [1:2038] "'t Hart LM" "Aaby P" "Aadahl M" "Aagaard-Hansen J" ...
Subset Authors
- Include authors, who have more than one publication.
is.included <- diag( adjacency.mat ) > 1
data.plot <- adjacency.mat[ is.included, is.included ]
str( data.plot )
## num [1:468, 1:468] 2 0 0 0 0 0 2 0 2 0 ...
## - attr(*, "dimnames")=List of 2
## ..$ : chr [1:468] "'t Hart LM" "Aagaard-Hansen J" "Adam T" "Adam TC" ...
## ..$ : chr [1:468] "'t Hart LM" "Aagaard-Hansen J" "Adam T" "Adam TC" ...
Wrap Author Names
- Add line break upon whitespace.
- Add line break upon dash.
names <- rownames( data.plot )
names <-
stringr::str_replace_all(
string = names,
pattern = "\\s",
replacement = "\n"
)
names <-
stringr::str_replace_all(
string = names,
pattern = "\\-",
replacement = "-\n"
)
names <-
stringr::str_replace_all(
string = names,
pattern = "\\n\\-",
replacement = ""
)
names( names ) <- rownames( data.plot )
head( names )
## 't Hart LM Aagaard-Hansen J Adam T
## "'t\nHart\nLM" "Aagaard-\nHansen\nJ" "Adam\nT"
## Adam TC Afsar B Agarwal R
## "Adam\nTC" "Afsar\nB" "Agarwal\nR"
Create a Network Representation of the Adjacency Matrix
- Create a network representation of the adjacency matrix with the network package.
- The network should be non-directional.
net.network <-
network::network(
x = data.plot,
directed = FALSE
)
Lay Out the Network
- Lay out the network on a two-dimensional plane (i.e., page) using the ggnetwork package.
ggnetwork <- ggnetwork::ggnetwork( x = net.network )
head( ggnetwork )
## x y vertex.names xend yend
## 1 0.000000000 0.3325604 Mygind E 0.059466626 0.3103337
## 2 0.000000000 0.3325604 Mygind E 0.103467979 0.3401734
## 3 0.000000000 0.3325604 Mygind E 0.003035168 0.3527912
## 4 0.002999419 0.3112239 Mygind L 0.059466626 0.3103337
## 5 0.002999419 0.3112239 Mygind L 0.000000000 0.3325604
## 6 0.002999419 0.3112239 Mygind L 0.103467979 0.3401734
Define Additional Properties for the Visualization
- Define properties of the network:
- Degree: number of vertices (i.e., connections) from each node (here: number of publications for each author)
- Size: size of each node in the visualization (here: based on degree)
- Label: Name of each node (here: author) to show in the visualization
- Text: Additional information to show for each node on hover
- Name of the node (here: author)
- Degree of the node (here: number of publications)
- Number of neighbors to the node (here: number of co-authors)
ggnetwork$"degree" <- diag( data.plot )[ ggnetwork$"vertex.names" ]
ggnetwork$"size" <- ggnetwork$"degree" * 10
ggnetwork$"name.formatted" <- names[ ggnetwork$"vertex.names" ]
tmp <- rowSums( data.plot > 0 ) - 1
ggnetwork$"N.neighbors" <- tmp[ ggnetwork$"vertex.names" ]
ggnetwork$"text" <-
paste0(
ggnetwork$"vertex.names",
":\n\t",
ggnetwork$"degree",
" publications",
"\n\t",
ggnetwork$"N.neighbors",
" co-authors"
)
head( ggnetwork )
## x y vertex.names xend yend degree size
## 1 0.000000000 0.3325604 Mygind E 0.059466626 0.3103337 2 20
## 2 0.000000000 0.3325604 Mygind E 0.103467979 0.3401734 2 20
## 3 0.000000000 0.3325604 Mygind E 0.003035168 0.3527912 2 20
## 4 0.002999419 0.3112239 Mygind L 0.059466626 0.3103337 4 40
## 5 0.002999419 0.3112239 Mygind L 0.000000000 0.3325604 4 40
## 6 0.002999419 0.3112239 Mygind L 0.103467979 0.3401734 4 40
## name.formatted N.neighbors text
## 1 Mygind\nE 5 Mygind E:\n\t2 publications\n\t5 co-authors
## 2 Mygind\nE 5 Mygind E:\n\t2 publications\n\t5 co-authors
## 3 Mygind\nE 5 Mygind E:\n\t2 publications\n\t5 co-authors
## 4 Mygind\nL 7 Mygind L:\n\t4 publications\n\t7 co-authors
## 5 Mygind\nL 7 Mygind L:\n\t4 publications\n\t7 co-authors
## 6 Mygind\nL 7 Mygind L:\n\t4 publications\n\t7 co-authors
Create the Basic Visualization
- Using the ggplot2 package with rendering of the nodes and edges from the ggnetwork package.
plot <-
ggplot2::ggplot(
data = ggnetwork,
mapping =
ggplot2::aes(
x = x,
y = y,
xend = xend,
yend = yend
)
) +
ggnetwork::geom_edges() +
ggnetwork::geom_nodes()
plot
Create Visualization with Additional Properties
- Add additional properties:
- Text for tooltip (used later in the interactive version)
- Formatted names of the nodes (here: authors)
- Transparent edges
- Node size according to the degree of the node (here: number of publications)
- Simple white colour theme
plot <-
ggplot2::ggplot(
data = ggnetwork,
mapping =
ggplot2::aes(
x = x,
y = y,
xend = xend,
yend = yend,
label = name.formatted,
text = text
)
) +
ggnetwork::geom_edges( alpha = 0.125 ) +
ggnetwork::geom_nodes(
mapping =
ggplot2::aes(
size = size
)
) +
ggnetwork::geom_nodetext(
alpha = 0.25,
size = 3
) +
ggthemes::theme_solid()
plot
Create the Interactive Visualization
- Create an interactive version of the visualization with the ggplotly function from the plotly package.
- Show info text about an author on hover-over.
plotly::ggplotly(
p = plot,
tooltip = c( "text" )
)